Whoops, I meant a 'function in ape?' -Dave On Mon, Jun 15, 2015 at 10:26 AM, David Bapst <[email protected]> wrote: > Hi Brian, > > I was already aware of the read.tree(write.tree()) fix, however I've > run into (corner?) cases where a particular sorting of edges or > whatever can lead to a loss of tip taxa using the > read.tree(write.tree()) approach; plus, read.tree(write.tree()) gets > completely flabbergasted by singleton nodes... > > Emmanuel, will checkValidPhylo be made a function in R? It something > I'd certainly like to call for my own internal > phylogeny-object-cleaning functions... > > Cheers, > -Dave > > On Mon, Jun 15, 2015 at 9:49 AM, Brian O'Meara <[email protected]> wrote: >> A kludgy solution to achieve Dave's original use case of fixing >> not-quite-right phylo objects is to do: >> >> phy <- read.tree(text=write.tree(phy)) >> >> It converts the tree to Newick and reads it back in. >> >> It's not as good a solution as using a validator (great addition, Emanuel!) >> to find and fix the general problem, but it can help in a pinch. >> >> Best, >> Brian >> >> >> _______________________________________ >> Brian O'Meara >> Assistant Professor >> Dept. of Ecology & Evolutionary Biology >> U. of Tennessee, Knoxville >> http://www.brianomeara.info >> >> Postdoc collaborators wanted: http://nimbios.org/postdocs/ >> Calendar: http://www.brianomeara.info/calendars/omeara >> >> On Mon, Jun 15, 2015 at 11:29 AM, Emmanuel Paradis <[email protected]> >> wrote: >>> >>> Hi David, >>> >>> collapse.singles() seems to work correctly if the "phylo" object is >>> correctly conformed. Some features of this class may seem annoying (and >>> Klaus and I alredy discussed about this), but these help for other things. >>> As a reminder the class "phylo" is defined here: >>> >>> http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf >>> >>> Recently, I put a function on github to help code writters: >>> >>> https://github.com/emmanuelparadis/checkValidPhylo >>> >>> This could help you to detect problems that would be tough to find >>> otherwise. >>> >>> Cheers, >>> >>> Emmanuel >>> >>> >>> Le 12/06/2015 22:41, David Bapst a écrit : >>>> >>>> Hi Klaus (and others), >>>> >>>> Ah, I see! The real bug then appears to be in collapse.singles, as it >>>> does not reorder the ID numbers in $edge. Here's a quick function to >>>> return the root ID: >>>> >>>> getRootID<-function(tree){ >>>> uniqueNode<-unique(tree$edge[,1]) >>>> whichRoot<-sapply(uniqueNode,function(x) >>>> (sum(x==tree$edge[,2])==0)) >>>> rootID<-uniqueNode[whichRoot] >>>> return(rootID) >>>> } >>>> >>>> And if we run it... >>>> >>>>> getRootID(tree) #original tree >>>> >>>> [1] 151 >>>>> >>>>> getRootID(tree1) #after collapse.singles >>>> >>>> [1] 151 >>>>> >>>>> getRootID(tree2) #after reorder.phylo >>>> >>>> [1] 131 >>>> >>>> And we can see that although the number of nodes certainly changed >>>> when collapse.singles was run, it didn't change the root node's ID. >>>> >>>> So I guess this is really a collapse.singles bug report. Thanks for >>>> the insight, Klaus! >>>> >>>> -Dave >>>> >>>> On Fri, Jun 12, 2015 at 2:27 PM, Klaus Schliep <[email protected]> >>>> wrote: >>>>> >>>>> Hi David, >>>>> >>>>> I found the bug. Somehow ape assumes on the one hand that the root is >>>>> number >>>>> of tips + 1. >>>>> On the other hand the root of an phylo object is the node which is in >>>>> tree$edge[,1], but not in tree$edge[,2], >>>>> this is the case even in an unrooted tree. This annoys me for a long >>>>> time. >>>>> >>>>> The root of tree1 with the definition above is actually node 151 and not >>>>> 131. Changing these solves your problem: >>>>> Here is a small function to do this for you: >>>>> >>>>> switch.nodes<- function(tree, a, b){ >>>>> ntips = length(tree$tip.label) >>>>> tree$edge[tree$edge==a] = 0L >>>>> tree$edge[tree$edge==b] = as.integer(a) >>>>> tree$edge[tree$edge==0L] = as.integer(b) >>>>> if(!is.null(tree$node.label)){ >>>>> tmp<-tree$node.label[a-ntips] >>>>> tree$node.label[a-ntips] = tree$node.label[b-ntips] >>>>> tree$node.label[b-ntips] = tmp >>>>> } >>>>> tree >>>>> } >>>>> >>>>> library(phangorn) >>>>> attr(tree1, "order") = NULL >>>>> getRoot(tree1) >>>>> >>>>> tree2 = switch.nodes(tree1, 131, 151) >>>>> plot(tree2) # now works for me >>>>> >>>>> Cheers and have a nice weekend, >>>>> Klaus >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Fri, Jun 12, 2015 at 2:53 PM, David Bapst <[email protected]> wrote: >>>>>> >>>>>> >>>>>> Hello all, >>>>>> >>>>>> As those of you who directly manipulate the guts of phylo objects in >>>>>> your code (or construct new phylo objects whole cloth from >>>>>> un-phylo-like data structures) have probably experienced, it is >>>>>> sometimes easy to create $edge matrices that aren't accepted by ape >>>>>> functions (I often use plot.phylo as my litmus for this). >>>>>> >>>>>> When this occurs, various things can be done; I usually do the >>>>>> following sequence: >>>>>> >>>>>> collapse.singles() >>>>>> reorder.phylo(,"cladewise") >>>>>> read.tree(text=write.tree(,file=NULL)) >>>>>> >>>>>> ...or something along those lines. >>>>>> >>>>>> However, I've run into an issue where reorder.phylo() returns what is >>>>>> essentially a scrap of the original $edge matrix, without warning. >>>>>> Very worrisome! I'm using R version 3.2.0 and ape 3.3. Here's, my >>>>>> script, including a call to a saved object on my website, so that the >>>>>> error can be reproduced: >>>>>> >>>>>> (Why do I have an .Rdata object listed with a .txt extension, you >>>>>> might wonder? Because my school apparently sanitizes file extensions >>>>>> on our hosted websites that it thinks are executables, archives or >>>>>> doesn't recognize, but doesn't bother to check file innards when it >>>>>> does recognize the extensions. Its easily hacked, at least.) >>>>>> >>>>>> ################# >>>>>> >>>>>> library(ape) >>>>>> >>>>>> load(url("http://webpages.sdsmt.edu/~dbapst/weirdTree_06-12-15.txt";)) >>>>>> >>>>>> #can I plot it? >>>>>> plot(tree) >>>>>> #nope >>>>>> >>>>>> tree1<-collapse.singles(tree) >>>>>> >>>>>> #any single-child nodes left? >>>>>> sum(sapply(unique(tree1$edge[,1]),function(x) >>>>>> sum(x==tree1$edge[,1])==1)) >>>>>> #nope >>>>>> >>>>>> #can I plot it? >>>>>> plot(tree1) >>>>>> #nope >>>>>> >>>>>> #now reorder >>>>>> tree2<-reorder.phylo(tree1,"cladewise") >>>>>> tree2$edge >>>>>> >>>>>> #now reorder with postorder >>>>>> tree2<-reorder.phylo(tree1,"postorder") >>>>>> tree2$edge >>>>>> >>>>>> ################# >>>>>> >>>>>> As we can see, reorder.phylo with various ordering methods returns an >>>>>> edge matrix with just six rows, from a tree that originally had >>>>>> hundreds of edges. Most worrisome, it does this without any error >>>>>> message. In this particular case, I retain the tree correctly if I >>>>>> skip reorder.phylo and use the read.tree(write.tree) trick, but this >>>>>> behavior of reorder.phylo is worrying. >>>>>> >>>>>> Anyone have a clue what's going on here? If I am perhaps misusing >>>>>> reorder.phylo(), is there an alternative approach for use in cleaning >>>>>> phylo objects? >>>>>> >>>>>> Cheers, >>>>>> -Dave >>>>>> >>>>>> -- >>>>>> David W. Bapst, PhD >>>>>> Adjunct Asst. Professor, Geology and Geol. Eng. >>>>>> South Dakota School of Mines and Technology >>>>>> 501 E. St. Joseph >>>>>> Rapid City, SD 57701 >>>>>> >>>>>> http://webpages.sdsmt.edu/~dbapst/ >>>>>> http://cran.r-project.org/web/packages/paleotree/index.html >>>>>> >>>>>> _______________________________________________ >>>>>> R-sig-phylo mailing list - [email protected] >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>>>>> Searchable archive at >>>>>> http://www.mail-archive.com/[email protected]/ >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Klaus Schliep >>>>> Postdoctoral Fellow >>>>> Revell Lab, University of Massachusetts Boston >>>>> >>>> >>>> >>>> >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - [email protected] >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> Searchable archive at >>> http://www.mail-archive.com/[email protected]/ >> >> > > > > -- > David W. Bapst, PhD > Adjunct Asst. Professor, Geology and Geol. Eng. > South Dakota School of Mines and Technology > 501 E. St. Joseph > Rapid City, SD 57701 > > http://webpages.sdsmt.edu/~dbapst/ > http://cran.r-project.org/web/packages/paleotree/index.html
-- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
